Ogas - page 1 of 40 CURRICULUM VITAE JOSEPH P. OGAS PROFESSOR OF BIOCHEMISTRY Present Address: Department of Biochemistry 175 South University Street Purdue University West Lafayette, Indiana 47907-2063 (765) 496-3969 (765) 494-7897 (fax) [email protected]Place of Birth: San Francisco, California, U.S.A. EDUCATION: 1982-1986 B.S. Stanford University, Stanford, California B.S. in Chemistry 1986-1992 Ph.D. University of California at San Francisco, San Francisco, California Department of Biochemistry and Biophysics Ph.D. Advisor: Dr. Ira Herskowitz Part II: “GENERAL INFORMATION” a. Academic and Administrative Appointments 2019-present Professor, Department of Biochemistry, Purdue University, West Lafayette, Indiana 2018-present Associate Head, Department of Biochemistry, Purdue University, West Lafayette, Indiana 2018-present Associate Director, Purdue University Center for Cancer Research 2004-2019 Associate Professor, Department of Biochemistry, Purdue University, West Lafayette, Indiana 1998-2004 Assistant Professor, Department of Biochemistry, Purdue University, West Lafayette, Indiana
Transcript
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CURRICULUM VITAE
JOSEPH P. OGAS
PROFESSOR OF BIOCHEMISTRY Present Address: Department of Biochemistry
175 South University Street Purdue University
West Lafayette, Indiana 47907-2063 (765) 496-3969 (765) 494-7897 (fax) [email protected] Place of Birth: San Francisco, California, U.S.A. EDUCATION: 1982-1986 B.S. Stanford University, Stanford, California B.S. in Chemistry 1986-1992 Ph.D. University of California at San Francisco, San Francisco, California Department of Biochemistry and Biophysics Ph.D. Advisor: Dr. Ira Herskowitz Part II: “GENERAL INFORMATION” a. Academic and Administrative Appointments 2019-present Professor, Department of Biochemistry, Purdue University, West Lafayette, Indiana 2018-present Associate Head, Department of Biochemistry, Purdue University, West Lafayette,
Indiana 2018-present Associate Director, Purdue University Center for Cancer Research 2004-2019 Associate Professor, Department of Biochemistry, Purdue University, West Lafayette, Indiana 1998-2004 Assistant Professor, Department of Biochemistry, Purdue University, West Lafayette, Indiana
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1994-1998 Research Associate, Carnegie Institution of Washington, Department of Plant Biology, Stanford, California. Post-doctoral advisor: Dr. Chris Somerville 1992-1993 Research Associate, Michigan State University - Department of Energy Plant Research Laboratory, East Lansing, Michigan. Post-doctoral advisor: Dr. Chris Somerville e. Awards and Honors 2016-2017 College of Agriculture Outstanding Counselor Award 1992-1995 National Science Foundation Postdoctoral Research Fellow in Plant Biology 1991-1992 Ford Foundation Dissertation Year Fellow 1991-1992 University of California Scholarship in Biochemistry 1989-1991 Supported by NIH Institutional Training Grant in Molecular and Cell Biology 1986-1989 National Science Foundation Graduate Fellow 1984-1986 National Chicano Council on Higher Education Science Fellow 1984-1986 Kodak Scholar in Chemistry for Class of 1986 1983 Recipient of The President's Award for Academic Excellence
1982-1986 National Merit Scholar Part II: Section A “DISCOVERY” 1a.(1) Published Work (Peer Reviewed)
Note: In general, tier rankings for promotion documents in the Department of Biochemistry are linked to impact factors, but faculty are given the opportunity to make tier designations that are most accurate and appropriate for their own subfield of the discipline. Note: For non-corresponding author publications at Purdue, details of Dr. Ogas’s contributions are stated. All publications can be conveniently accessed through Dr. Ogas’ MyBibliography: https://www.ncbi.nlm.nih.gov/sites/myncbi/joseph.ogas.1/bibliography/41153483/public/?sort=date&direction=ascending Google Scholar Citations = 2930, h-index = 18, i10-index = 20 (as of August, 2018)
Sorlien EL, †Witucki MA, and *Ogas J (2018). Efficient Production and Identification of CRISPR/Cas9-Generated Gene Knockouts in the Model System Danio rerio. J. Vis. Exp (138), e56969, doi:10.3791/56969 2nd Quartile Tier Ranking SciMago; 2015/2016 Impact Factor: 1.23; # citations = 0
1st Quartile Tier Ranking SciMago; 2012 ISI Impact Factor = 5.46; # citations = 20 Zhang H, Bishop B, †Ringenberg W, Muir B, *Ogas J (2012). The CHD3 remodeler PICKLE associates with genes enriched for trimethylation of histone H3 lysine 27. Plant Physiology 159:418. 1st Quartile Tier Ranking SciMago; 2012 ISI Impact Factor = 6.16; # citations = 75 Muir WM, Rosa GJM, Pittendrigh BR, Xu Z, Rider SD, Fountain M, and *Ogas J (2009). A mixture model approach for the analysis of small exploratory microarray experiments. Computational Statistics and Data Analysis 53:1566. 2nd Quartile Tier Ranking SciMago; 2009 ISI Impact Factor = 1.23; # citations = 5 Contribution: Generated all data used for validation of statistical approach. Zhang H, Rider SD, Henderson J, Fountain M, Chuang K, Kandachar K, †Simons A, Edenberg HJ, Romero-Severson J, Muir WM, and *Ogas J (2008). The CHD3 remodeler PICKLE promotes trimethylation of histone H3 lysine 27. J Biol Chem 283:22637. 1st Quartile Tier Ranking SciMago; 2008 ISI Impact Factor = 5.52; # citations = 67
Muir WM, Romero-Severson J, Rider SD, †Simons A, and *Ogas J (2006). Application of One Sided t-tests and a Generalized Experiment Wise Error Rate to High-Density Oligonucleotide Microarray Experiments: An Example Using Arabidopsis. J Data Sci 4:323. # citations = 5 Contribution: Generated all data used for validation of statistical approach. Li H-C, Chuang K., Henderson JT, Rider Jr SD, Bai Y, Zhang H, Fountain M, †Gerber J, and *Ogas J (2005). PICKLE acts during germination to repress expression of embryonic traits. Plant Journal 44:1010. 1st Quartile Tier Ranking SciMago; 2005 ISI Impact Factor = 6.97; # citations = 59 Falcone DL, Ogas JP, and *Somerville CR (2004). Regulation of membrane fatty acid composition by temperature in mutants of Arabidopsis with alterations in membrane lipid composition. BMC Plant Biology 4:17. 1st Quartile Tier Ranking SciMago; 2013 ISI Impact Factor = 4.35; # citations = 204 Rider SD, Hemm MR, Hostetler HA, Li H.-C., Chapple C, and *Ogas J (2004). Metabolic profiling of the Arabidopsis pkl mutant reveals selective derepression of embryonic traits. Planta 219:489-99. 1st Quartile Tier Ranking SciMago; 2004 ISI Impact Factor = 3.11; # citations = 27 Hemm MR, Rider SD, Ogas J, Murry DJ, and *Chapple C (2004). Light induces phenylpropanoid metabolism in Arabidopsis roots. Plant J. 38:765-78. 1st Quartile Tier Ranking SciMago; 2004 ISI Impact Factor = 6.37; # citations = 130 Contribution: Carried out qRT-PCR analysis of relative transcript levels of genes for figure in manuscript. Henderson JT, Li H-C, Rider SD, Mordhorst AP, Cheng JC, Romero-Severson J, Cheng J-C, †Robey J, Sung ZR, de Vries SC, and *Ogas J (2004). PICKLE Acts throughout the Plant to Repress Expression of Embryonic Traits and May Play a Role in Gibberellin-Dependent Responses. Plant Physiol 134:995-
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1005. This article was selected to be highlighted at the front of the journal in the “On the inside” section. 1st Quartile Tier Ranking SciMago; 2004 ISI Impact Factor = 5.88; # citations = 91 Rider SDR, Henderson JT, Jerome RE, Edenberg HJ, Romero-Severson J, and *Ogas J (2003). Coordinate repression of regulators of embryonic identity by PICKLE during germination of Arabidopsis. Plant J. 35:33-43. 1st Quartile Tier Ranking SciMago; 2003 ISI Impact Factor = 5.91; # citations = 111 Ogas J, Kaufmann S, Henderson J, and Somerville C (1999). PICKLE is a CHD3 chromatin-remodeling factor that regulates the transition from embryonic to vegetative development in Arabidopsis. Proc. Natl. Acad. Sci. USA 96:13839-13844. Top tier journal; 1999 ISI Impact Factor = 10.26; # citations = 327
Ogas J, Cheng J-C, Sung ZR, and *Somerville C (1997). Cellular differentiation regulated by gibberellin in the Arabidopsis thaliana pickle mutant. Science 277:91-94. Times cited = 215 Gray JV, Ogas JP, Kamada Y, Stone M, Levin DE, and *Herskowitz I (1997). A role for the Pkc1 MAP kinase pathway of Saccharomyces cerevisiae in bud emergence and identification of a putative upstream regulator. EMBO J. 16:4924-4937. Times cited = 185 Measday V, Moore L, Ogas J, Tyers M, and *Andrews B (1994). The PCL2 (ORFD)-PHO85 cyclin-dependent kinase complex: a cell cycle regulator in yeast. Science 266:1391-1395. Times cited = 151 ‡Espinoza FH, ‡Ogas J, Herskowitz I, and *Morgan DO (1994). Cell cycle control by a complex of the cyclin HCS26 (PCL1) and the kinase PHO85. Science 266:1388-1391. Times cited = 128 Herskowitz I, Andrews B, Kruger W, Ogas J, Sil A, Coburn C, and Peterson C (1992). Integration of multiple regulatory inputs in the control of HO expression in yeast. In Transcriptional Regulation (ed. SL Knight and KR Yamamoto), pp. 949-974. Cold Spring Harbor Laboratory Press, Cold Spring Harbor, New York. Ogas J, Andrews BJ, and *Herskowitz I (1991). Transcriptional activation of CLN1, CLN2, and a putative new G1 cyclin (HCS26) by SWI4, a positive regulator of G1-specific transcription. Cell 66:1015-1026. Times cited = 277 Herskowitz I, Ogas J, Andrews BJ, and Chang F (1991). Regulators of synthesis and activity of the G1 cyclins of budding yeast. In Cold Spring Harbor Symposium On Quantitative Biology, The Cell Cycle; (pp. 33-40). Cold Spring Harbor Laboratory Press. Times cited = 3
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1a.(2) Published Work (Invited Reviews) Zhang H and *Ogas J (2009). An epigenetic perspective on developmental regulation of seed genes. Molecular Plant 2:610-27. 1st Quartile Tier Ranking SciMago; 2009 ISI Impact Factor = 2.78; # citations = 42 *Ogas J (2007). Preface to special issue on plant chromatin: Structure and expression. Biochim Biophys Acta 1769:267-8. 1st Quartile Tier Ranking SciMago; 2003 ISI Impact Factor = 5.91; # citations = 0 *Ogas J (2000). Gibberellins. Current Biology 10: R48-R48. 1st Quartile Tier Ranking SciMago; 2000 ISI Impact Factor = 8.39; # citations = 10 *Ogas J (1998). Plant hormones: Dissecting the gibberellin response pathway. Current Biology 8:R165-R167. 1st Quartile Tier Ranking SciMago; 1998 ISI Impact Factor = 7.86; # citations = 8
1b.(1) Submitted Work Under Review 1b.(2) Submitted Work Under Revision
1e. Work in Progress
Bishop B, Carter B, Sorlien E, †Zelten Z, Long J, and *Ogas J. The CHD chromatin remodeler PICKLE contributes to repair of DNA double-strand breaks in Arabidopsis.
2. Exhibition of Creative Work 3. Other Evidence of Creative Excellence
Patents Filed Ogas J, and Somerville C. “Methods and compositions for regulating developmental identity” PCT patent application, Purdue Ref. P-99059.00.WO Mittendorf V, Haertel H, Ogas J. “Sugar and lipid metabolism regulators in plants V”. PCT patent application, Purdue Ref. P-03048.00.WO
4. Presentations
Invited Lectures (External) Mid-West Regional Society for Developmental Biology Meeting, Case Western Reserve University, Ohio, September, 2018. Identification of novel players and strategies for building and maintaining repressive chromatin in plants. Nanjing Agricultural University, Nanjing, China, November 2016. A novel role for CHD remodelers in H3K27me3-dependent gene expression in plants.
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Shanghai Center for Plant Stress Biology (PSC), Shanghai, China, November 2016. A novel role for CHD remodelers in H3K27me3-dependent gene expression in plants. Bonn University, Bonn, Germany, July 2016. A novel role for CHD remodelers in H3K27me3-dependent gene expression in plants. Dusseldorf University, Dusseldorf, Germany, July 2016. A novel role for CHD remodelers in H3K27me3-dependent gene expression in plants. Midwest Chromatin and Epigenetics Meeting, Grand Rapids, MI, June 2016. Dissecting the contribution of CHD3 remodelers to the epigenome and developmental identity in Arabidopsis. Department of Biochemistry and Molecular Biology, Wright State University, Ohio, September 2010. Role of CHD3 chromatin remodelers in gene expression in Arabidopsis. Agriculture and Agri-Food Canada, London Canada, November 2009. Role of CHD3 proteins in epigenetic regulation of seed genes in Arabidopsis. Plant Growth Regulation Society of America Annual Meeting, Quebec, Canada, July 2006. Role of gibberellin and PICKLE in determination of developmental identity. Division of Natural Sciences and Mathematics, Wesleyan University, Indiana, April 2006. Invited to give 2 presentations to undergraduates in a Cell Biology class and in a Biochemistry class. The title of the presentation for the Cell Biology class was “Determination of when a chromatin factor regulates developmental identity”. The title of the presentation for the Biochemistry class was “Use of microarray analysis to identify targets of a chromatin remodeling factor”. (Activity also listed under ENGAGEMENT #6 Advising, Counseling, and Recruiting Students.) Division of Natural Sciences and Mathematics, Wesleyan University, Indiana, April 2005. Invited to give 2 presentations to undergraduates in a Cell Biology class and in a Biochemistry class. The title of the presentation for the Cell Biology class was “Determination of when a chromatin factor regulates developmental identity”. The title of the presentation for the Biochemistry class was “Use of microarray analysis to identify targets of a chromatin remodeling factor”. (Activity also listed under ENGAGEMENT #6 Advising, Counseling, and Recruiting Students.) School of Biological Sciences, University of Manchester, United Kingdom, October 2003. A microarray-based strategy for identification of targets of a CHD3-chromatin remodeling factor. Department of Biology, University of York, United Kingdom, October 2003. PICKLE, gibberellin, and germination in Arabidopsis. Department of Cell and Developmental Biology, John Innes Centre, United Kingdom, October 2003. PICKLE, gibberellin, and germination in Arabidopsis.
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Department of Plant Sciences, Oxford, United Kingdom, October 2003. PICKLE, gibberellin, and germination in Arabidopsis. DNA LandMarks Inc. Montreal, Canada August 2002. Role of PICKLE and of gibberellin in repression of embryonic identity in Arabidopsis. Cold Spring Harbor Laboratory course in Arabidopsis Molecular Genetics, Cold Spring Harbor, New York, July 2002. Lecture I: Embryogenesis in Arabidopsis. Lecture II: Role of PKL in repression of embryonic identity. The Society for Experimental Biology Annual Meeting (Epigenetic Section), Swansea, United Kingdom, April 2002. (invited, unable to attend) BASF Plant Science LLC, Research Triangle Park, North Carolina, October 2001. The role of a CHD3 chromatin remodeling factor in establishing repression of embryonic identity in Arabidopsis. School of Biological Sciences, University of Manchester, United Kingdom, May 2001. Gibberellin, chromatin remodeling, and determination during germination of Arabidopsis. Jacques Monod Conference on "Signalling Processes during Plant Development" Presqu'ile de Giens, France May 2001. The role of a CHD3 chromatin remodeling factor in establishing repression of embryonic identity in Arabidopsis. Department of Agronomy, University of Kentucky, March 2001. The role of a CHD3 chromatin remodeling factor in establishing repression of embryonic identity in Arabidopsis. Biochemistry and Molecular Biology Department, Michigan State University, December 2000. The role of a CHD3 chromatin remodeling factor in establishing repression of embryonic identity in Arabidopsis. Biochemistry and Molecular Biology, Indiana University School of Medicine, November 1999. Regulation of developmental identity by a CHD3 chromatin remodeling factor in Arabidopsis. RIKEN, Tsuba, Japan, June 1999. PKL is a component of a GA signaling pathway that regulates a developmental switch during germination. RIKEN, Wako-shi, Japan, June 1999. PKL is a component of a GA signaling pathway that regulates a developmental switch during germination. BASF, Ludwigshafen, Germany, June 1999. The role of GA and PKL in establishing repression of embryonic identity. Division of Biological Sciences, University of Missouri, Columbia, MO, December 1998. GA and PKL are involved in a developmental switch during germination.
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Monsanto, St. Louis, MO, December 1998. Regulation of developmental identity by gibberellin and chromatin remodeling in Arabidopsis thaliana. FASEB meeting on Plant Developmental Mechanisms, Saxton’s River, Vermont, August 1998. Regulation of cell identity by gibberellin in the Arabidopsis pickle mutant.
Invited Lectures (Internal) Indiana CTSI Retreat at Purdue University: Assistive Technologies for Healthcare in January 2019, co-leader of breakout session titled “Cross-Cutting Biology – Bridging Models from Plants to Animals to Humans”. Purdue Institute for Integrative Neuroscience NeuroNetworking Summer Seminar Series, July 2018. Functional analysis of the Chd5 chromatin remodeler in neural differentiation and tumor suppression in zebrafish.
Purdue Center for Cancer Research, May 2015. Establishment of Danio rerio as a model system for functional analysis of the CHD5 tumor suppressor.
Department of Biochemistry, Purdue University, August 2011. Role of CHD3 chromatin remodelers in gene expression in Arabidopsis. Department of Biochemistry, Purdue University, November 2007. Role of a CHD3 chromatin remodeler in transcriptional repression in Arabidopsis. Department of Biochemistry, Purdue University, February 2005. PICKLE and the self-basting beet. Bioinformatics/Statistical Genetics Seminar Series, Purdue University, November 2004. Mastering the Microarray Mine Field: A Success Story. Dual presentation with Jeanne Romero-Severson Bioinformatics/Statistical Genetics Seminar Series, Purdue University, January 2003. A Microarray-Based Screen for Targets of a Chromatin Remodeling Factor in Arabidopsis. Department of Department of Horticulture and Landscape Architecture, Purdue University, November 2001. Gibberellin, chromatin remodeling, and determination during germination of Arabidopsis. Department of Chemistry, Purdue University, April 2001. The role of a CHD3 chromatin remodeling factor in establishing repression of embryonic identity in Arabidopsis. Department of Botany, Purdue University, West Lafayette, IN, February 1999. Regulation of developmental identity by gibberellin and chromatin remodeling in Arabidopsis. Posters Biology Honor Society Convention, San Juan, Puerto Rico, April 2019. Examining cross-talk between histone variant H2A.Z and the repressive epigenetic modification H3K27me3. Carlos Guzman Acevedo, Jiaxin Long, Joe Ogas.
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American Chemical Society Chemistry for New Frontiers, Orlando, Florida March 2019. Epigenetic Interactions Between Methyltransferase SWN and Chromatin Remodeler PKL. Joey Dean, Jiaxin Long, Joe Ogas. Arkansas IDeA Network of Biomedical Research Excellence, University of Arkansas, Fayetteville, Arkansas, November 2018. Epigenetic Interactions Between Methyltransferase SWN and Chromatin Remodeler PKL. Joey Dean, Jiaxin Long, Joe Ogas. Cell Symposia: Transcriptional Regulation in Development, Chicago, Illinois, July 2014. The chromatin remodeler chd5 promotes head development during embryogenesis of Danio rerio. Brett Bishop, Kim Tyler, Amanda Smith, Sylvia Bonilla, Yuk Fai Leung, and Joe Ogas. Midwest Chromatin and Epigenetics Meeting at University of Madison, Wisconsin, June 2014. Identification of a Role for CHD3 Remodelers in Fertilization and Seed Size in Arabidopsis. Ben Carter (presenter), Amanda Smith, Kyle McCarthy, Elisabeth Harris, Brian Dilkes, and Joe Ogas Midwest Chromatin and Epigenetics Meeting at University of Madison, Wisconsin, June 2014. Functional characterization of transgenic Danio rerio with altered expression of the chd5 chromatin remodeler. Erin Sorlien (presenter), Brett Bishop, Ben Carter, and Joe Ogas Midwest Chromatin and Epigenetics Meeting at University of Madison, Wisconsin, June 2014. The chromatin remodeler chd5 promotes head development during embryogenesis of Danio rerio. Brett Bishop, Kim Tyler, Amanda Smith, Sylvia Bonilla, Yuk Fai Leung, and Joe Ogas. Gordon Research Conference on “Epigenetics” at Stonehill College, Massachusetts, August 2011. The CHD3 remodeler PICKLE is targeted to genes enriched for trimethylation of histone H3 lysine 27. Brett Bishop (presenter), Heng Zhang, Whitney Ringenberg, Bill Muir, Joe Ogas Undergraduate Research Day, Purdue University, May 2006. GA-dependent accumulation of PKL protein in Arabidopsis thaliana. Courtney Chambers, James Henderson, Joe Ogas. Henderson JT and Ogas J. 2005. PKR2 is a CHD3 variant that functions redundantly with PKL to repress embryonic identity in Arabidopsis. Poster presented at the 2005 Sigma Xi Graduate Student Research Awards Competition. Arabidopsis Conference at Madison Wisconsin, June 2003. Microarray analysis of germinating pickle seedlings. Dean Rider, Jim Henderson, Vasundhara Kandachar, Alexis Simons, Jeanne Romero-Severson, Joe Ogas. Undergraduate Research Day, Purdue University, May 2003. Validation of Microarray Data Using quantitative-RT-PCR. Alexis Simons, Stanley Dean Rider, James Henderson, Jeanne Romero-Severson, Bill Muir, Joe Ogas.
Undergraduate Research Day, Purdue University, May 2003. Identification of GA signaling mutants by T-DNA mutagenized pickle mutant. Linda P. Quach, Hui-Chun Li, Joe Ogas.
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Gordon Conference on Quantitative Genetics and Genomics at Ventura California, February 2003. Analysis of Affymetrix® GeneChip® arrays: Significant vs. Real. Jeanne Romero-Severson, Bill Muir2 Stanley Dean Rider Jr., James Henderson, Joe Ogas Arabidopsis Conference at Madison Wisconsin, June 2001. Identification of the gibberellin signal transduction pathway that represses expression of embryonic identity in the pkl mutant of Arabidopsis. Hui-Chun Li, King Chuang, Katie English, Michelle Fredette, Kerry Behnke, Jim Henderson, Joe Ogas.
5. Involvement in Department Graduate Research Program
6. Grant Activities (Research grants and awards received) 6. 1. Current Grants (Research/Discovery) Note: Grants for Learning are provided later in Part II. Source and role: Center for Plant Biology Seed Grant (PI) Title: Determining the contribution of the Mediator complex to the repressive chromatin modification H3K27me3 in Arabidopsis Total project period and amount of award: 1/01/2019-12/31/2019, $50,000 6. 2. Pending Grants Source and role: National Science Foundation (PI) Title: Functional analysis of a novel epigenetic pathway incorporating a CHD chromatin remodeler, the
histone variant H2A.Z, and the repressive modification H3K27me3 Total project period and amount of award: 1/01/2020 – 12/31/2022, $916,833 6. 3. Past Grants Source and role: National Science Foundation (PI) Title: Understanding the contribution of a chromatin remodeler to regulation of tissue-specific gene
expression in Arabidopsis plants Total project period and amount of award: 6/01/2014-05/31/2018, $786,000 Source and role: AgSeed (PI) Title: Establishing a new animal system for discovering novel treatments for aggressive tumors Total project period and amount of award: 3/01/2015-12/31/2018, $75,000 Source and role: Purdue University Center for Cancer Research (co-PI) Title: The tumor suppressor CHD5 determines roscovitine sensitivity in SH-SY5Y neuroblastoma cells Total project period and amount of award: 4/01/2018-03/30/2019, $15,000 (responsible for $12,000) Source and role: Purdue University Center for Cancer Research (PI) Title: Proposal for Shared Resource Project for RNA-seq to identify genes that exhibit expression that is
dependent on the tumor suppressor Chd5 Total project period and amount of award: 5/01/2018-010/31/2018, $9,904 Source and role: National Institutes of Health (PI) Title: Determination of the role of CHD5 tumor suppressor in the zebrafish model Total project period and amount of award: 12/01/2013-11/30/2016, $352,770 Source and role: Purdue University Center for Cancer Research (PI) Title: CHD5 promotes H2A.Z and contributes to gene expression in neuroblastoma SH-SY5Y cells
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Total project period and amount of award: 9/22/2015-6/30/2016, $10,000 Source and role: National Science Foundation (PI) Title: Dissecting the Relationship between a CHD3 Chromatin Remodeler and the Repressive Epigenetic
Mark H3K27me3 in Arabidopsis Total project period and amount of award: 09/01/2009-08/31/2012, $330,000 Source and role: Showalter Research Trust Fund (co-PI) Title: Role of the CHD5 chromatin remodeler in zebrafish development – a potential tumorigenesis model Total project period and amount of award: 07/01/2009-06/30/2010, $75,000 (responsible for 50%) Source and role: Purdue Research Foundation (PI) Title: Biochemical characterization of the PKL chromatin remodeling complex Total project period and amount of award: 06/01/07 – 05/31/08, $14,627 Source and role: Purdue Research Foundation (PI) Title: Biochemical characterization of the PKL chromatin remodeling complex Total project period and amount of award: 06/01/06 – 05/31/07, $14,040 Source and role: Lemelson Foundation NCIIA (PI) Title: Application of pickle technology to oil production in radish Total project period and amount of award: 08/01/04 - 01/31/06, $17,700 Source and role: National Institutes of Health (PI) Title: Analysis of role of CHD proteins in Arabidopsis thaliana Total project period and amount of award: 04/01/00-03/31/06, $1,261,428 Source and role: BASF Plant Science LLC (PI) Title: Seed developmental studies in soybean grown in the field to identify genes capable of increasing seed
oil production Total project period and amount of award: 06/20/05 - 09/14/05, $5,939 Source and role: BASF Plant Science LLC (PI) Title: Cloning of genes that regulate oil production in Arabidopsis Total project period and amount of award: 04/01/03-03/31/04, $96,784 Source and role: Agricultural Research Project Assistantship (PI) Title: Identification and characterization of regulators of cell identity and/or gibberellin signal transduction
in Arabidopsis thaliana Total project period and amount of award: 01/01/03-12/31/04, $30,000 Source and role: Genomics Database Facility (co-PI) Title: Bioinformatics in the 21st century Total project period and amount of award: 2001-2004, $560,000 (responsible for 0%, meet with PI’s once a
year in advisory role)
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Source and role: BASF Plant Science LLC (PI) Title: Use of an activation-tagging strategy to identify genes capable of increasing seed oil production Total project period and amount of award: 04/01/00-03/31/03, $263,542 Source and role: National Institutes of Health (PI) Title: Analysis of role of CHD proteins in Arabidopsis thaliana Total project period and amount of award: 03/31/01, $36,480 Source and role: Purdue Research Foundation (PI) Title: Identification of transcriptional targets of a gibberellin signal transduction pathway in Arabidopsis Total project period and amount of award: 01/01/00-12/31/01, $23,332 Source and role: American Cancer Society - Purdue University Center for Cancer Research (PI) Title: Identification of the role of CHD chromatin remodeling factors in Saccharomyces cerevisiae Total project period and amount of award: 01/01/00-12/31/00, $20,000 Source and role: Purdue Department of Biochemistry Pilot Project (PI) Title: Identification of factors that mediate pheromone-dependent silencing of HO in Saccharomyces
cerevisiae Total project period and amount of award: 2001-2002, $25,000 7. Current Research Interests
Deciphering the role of CHD3/Mi-2 proteins as regulators of developmental transitions Dr. Ogas is a pioneer in the functional characterization of CHD3/Mi-2 chromatin remodeling factors.
CHD3/Mi-2 proteins are found throughout eukaryotes and are now known to play critical roles in development as key regulators of gene expression. Dr. Ogas was among the first to uncover a developmental role for CHD3/Mi-2 proteins when he discovered that PICKLE (PKL), a CHD3/Mi-2 gene in the model system Arabidopsis, was necessary for repression of embryonic identity. A tribute to the significance of this work is that it was cited by researchers working with C. elegans when describing their subsequent discovery of a role for CHD3/Mi-2 proteins during development in that model system.
CHD3/Mi-2 remodelers are now known to play a large number of roles in development, including determination of body plan in Drosophila, specification of somatic and germline cell identity in C. elegans, and as a critical tumor suppressor in humans. The research program of Dr. Ogas has expanded to reflect the growing awareness of the fundamental importance of CHD3/Mi-2 remodelers in differentiation and development in plants and animals. Dr. Ogas continues to exploit the singular aspects of PKL function in Arabidopsis to elucidate common mechanisms of developmental regulation by CHD3/Mi-2 proteins in eukaryotes. In addition, Dr. Ogas is now using the zebrafish model system to determine how the CHD3/Mi-2 protein CHD5 suppresses tumor formation in humans. Dr. Ogas combines genetic, biochemical, and genomic approaches within the context of the unique biology of each organism to seek fundamental insights into the mechanism of action of CHD3/Mi-2 remodelers with the goal of real world relevance.
Role of CHD3/Mi-2 remodelers in determination of developmental identity in plants Both plant and animal CHD3/Mi-2 remodelers play a critical role in repression of developmental
regulators, revealing that plants and animals have harnessed related remodelers to restrict expression of
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developmental regulators. Despite this conserved role, the Arabidopsis PKL remodeler acts via a distinct chromatin-based pathway. In animals, CHD3/Mi-2 remodelers act through the Mi-2/NuRD complex to promote histone deacetylation. In Arabidopsis, we have shown that PKL instead promotes levels of the repressive epigenetic mark H3K27me3. H3K27me3 plays an essential role in restricting expression of developmental identity genes to specific tissues in plants. Although we know that developmental identity is pliable in plants and have identified some of the factors employed to repress or activate tissue-specific genes, we know very little about the regulatory mechanisms and machinery that enables genes to transition from one state to another.
Based on multiple lines of evidence, we have proposed the existence of a new epigenetic pathway in plants by which PKL acts with PIE1 (a chromatin remodeler that promotes exchange of the histone variant H2A.Z) and CLF (a histone methyltransferase that deposits H3K27me3) to promote H3K27me3 homeostasis (Figure 1). Two unique features of this model are that H2A.Z is a component of H3K27me3-enriched chromatin and thereby enables deposition of H3K27me3 and that PKL contributes to H3K27me3 homeostasis by acting as a chromatin assembly factor. Thus, we propose that distinct mechanisms and factors are used to build and maintain H3K27me3-enriched chromatin in plants.
We have extensive experience in genetic and biochemical characterization of chromatin-associated factors in plants and have developed a unique set of transgenic lines and biochemical reagents. We are currently examining the robustness of our proposed model and characterizing the contributions of PKL and of PIE1 to other epigenetic features by using our unique collection of reagents to test the following hypotheses: 1) PKL and other CHD proteins contribute to chromatin assembly and epigenetic architecture. We propose that plants possess ATP-dependent chromatin remodelers that contribute to chromatin assembly in addition to the ISWI and CHD1 remodelers previously characterized in yeast and animal systems and that the corresponding assembly pathway contributes to maintenance of repressive epigenetic states. To test this hypothesis, we will generate recombinant versions of plant CHD and ISWI remodelers and examine prenucleosome maturation activity using recombinant plant histones in conjunction with phenotypic analysis of combinatorial mutants lacking these remodelers. We will couple these data with genome-wide studies that examine the effect of loss of PKL on nucleosome distribution and nucleosomal turnover. 2) Concurrent loss of PKL and PIE1 leads to a profound defect in levels of H2A.Z, H3K27me3, and/or other epigenetic features. We have shown
that plants carrying protein-null alleles of PKL and PIE1 exhibit extreme defects in organogenesis. The phenotype of this double mutant strongly suggests that these evolutionarily conserved remodeling factors have additional roles beyond that proposed by other labs and ourselves. To identify these roles, we will determine the associated epigenetic/expression phenotype of conditional pkl pie1 PKL-GR plants using RNA-seq, ChIP-seq, and MNase-seq. 3) Perturbation of H2A.Z is sufficient to alter the epigenetic/expression status of H3K27me3-enriched genes. A minimal explanation for the requirement of PIE1 for H3K27me3 is that the presence of H2A.Z promotes deposition of H3K27me3. Robust demonstration of such a role for H2A.Z in generation of H3K27me3 would provide a key insight into how H3K27me3-enriched chromatin is built in plants and suggest new mechanisms by which this critical repressor of developmental genes is regulated. To test this hypothesis,
Figure 1. A model depicting new relationships governing H3K27me homeostasis. (A) PIE1 promotes H3K27me3 deposition through H2A.Z exchange and (B) PKL promotes H3K27me3 retention through prenucleosome maturation after passage of an RNA or DNA polymerase.
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we will examine the effect of ablating genes that code for H2A.Z on the developmental/epigenetic phenotype of plants with regards to H3K27me3-dependent processes. We will also test the hypothesis that the PRC2 complex preferentially acts on nucleosomes containing H2A.Z using in vitro methyltransferase assays.
This research program has direct relevance to agriculture. Although plant developmental identity is generally regarded as easily altered in all plant species, in reality there are numerous plants for which developmental identity is not responsive to experimental manipulation. For example, many hardwood trees that are important agricultural crops are not amenable to biotechnical manipulation due to their rigid developmental identity. The proposed experiments will help elucidate a fundamental chromatin-based pathway that restricts developmental identity in plants and thus are likely to identify novel targets by which developmental identity can be manipulated in recalcitrant species. For example, we anticipate that a PKL-associated pathway promotes developmental identity in those plants that cannot be maintained by vegetative propagation (e.g. many hardwood trees) and that transient inhibition of this pathway would enable vegetative propagation of these species for the first time.
Role of the CHD5 remodeler in tumor suppression
Although epigenetic processes and chromatin-based phenomena have been shown to be critical factors in cancer etiology, a thorough mechanistic understanding of these processes is needed to provide therapies that can target tumor development and progression in cancer patients. Several studies have demonstrated that the chromatin remodeler CHD5 is a key tumor suppressor in humans. Spontaneous loss of CHD5 function is associated with formation of a wide range of tumors, including colorectal cancer, lung cancer, and leukemia. Loss of CHD5 plays a particularly significant role in development of neuroblastoma, which is the most common childhood extracranial solid tumor and is responsible for 15% of all cancer deaths in children. Reduced expression of CHD5 in a tumor is strongly correlated with a worse clinical outcome. Furthermore, restoration of CHD5 activity to cancer cells that lack CHD5 has been demonstrated to inhibit the growth potential of those cells. This last observation indicates that CHD5 can suppress growth of existing tumors and further suggests that medical strategies that augment CHD5 function will be effective in suppression of tumors that result from loss of CHD5. Development of such medical strategies requires an in depth understanding of the mechanism(s) by which CHD5 acts.
Substantial insight into the role of CHD5 as a tumor suppressor will likely be provided by understanding the contribution of CHD5 to H3K27me3 and neurogenesis. Studies in mice by other labs have revealed that knock-down of CHD5 results in defects in neurogenesis, neural outgrowth, and levels of H3K27me3 in differentiating neural cells. Further, CHD5 is unique among the highly-related CHD3/4/5 remodelers in that it is preferentially expressed in neural tissue and directly associates with H3K27me3. We undertook a phylogenetic analysis that revealed that CHD5 proteins are found only in vertebrates, which suggests a conserved function for the CHD5 remodeler in this lineage. We have therefore turned to zebrafish, a powerful vertebrate model system with an extensive toolbox, to facilitate identification and characterization of CHD5-dependent processes. Based on transient knock-down assays and expression analysis, we have already established that CHD5 is likely to play a similar role in both fish and in mammals.
Phenotypic characterization of CRISPR-generated chd5-/- fish in our lab has revealed that chd5-/- fish exhibit increased sensitivity to chemical inhibitors of epigenetic pathways and to a cyclin-dependent kinase inhibitor that preferentially acts on undifferentiated cells. Further, we have data indicating that loss of chd5 results in increased tumorigenesis in fish that also carry a mutant version of the well-characterized p53 tumor suppressor. Exploiting chd5-dependent phenotypes in conjunction with the powerful experimental tools available in zebrafish presents an ideal avenue by which to robustly test the following hypotheses regarding Chd5 remodelers in vertebrate neurogenesis and oncogenesis:
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1) chd5 contributes to both establishment and maintenance of neural differentiation states in multiple types of neurons. Expression of CHD5 is induced during neurogenesis and is also observed in differentiated neurons. We will use RNA-seq in the brains of wild-type and chd5-/- fish to determine the contribution of Chd5 remodelers to expression of transcriptional programs in differentiating and differentiated neurons. Comparative analysis of both mice and fish in which CHD5 has been knocked-down versus knocked out raises the possibility that the phenotype associated with loss of Chd5 remodelers is ameliorated by gene redundancy (e.g. the highly related CHD3 and CHD4 remodelers). To address this issue, we will generate an endogenous dominant negative allele of chd5 to more fully explore the role of Chd5 remodelers in neurogenesis. 2) chd5 enables crosstalk between DNA methylation and H3K27me3 in neurons. CHD5-related proteins typically function as a member of a multisubunit complex, and Chd5 from mouse brain is a component of a multisubunit Mi-2/NuRD-like complex. Mi-2/NuRD plays a major role in mediating histone deacetylation and transcriptional inactivation in response to DNA methylation in mammalian cells. Given previous characterization of Chd5 remodelers, we will examine DNA methylation and H3K27me3 genome-wide in neurons of wild-type and chd5 fish to examine the contribution of chd5 to these epigenetic features. In addition, we will use immunoprecipitation coupled to mass spectrometry (IP-MS) to identify proteins that interact with Chd5 in zebrafish embryos. 3) Loss of chd5 contributes to development of neuroblastoma in a MYCN-dependent zebrafish model. We have observed elevated rates of development of malignant peripheral neural sheath tumors (MPNST) in fish impaired for p53 and Chd5 after 18 months. Previous characterization in another lab of transgenic fish carrying the oncogene MYCN and impaired for the tumor suppressor NF1 resulted in strongly elevated rates of neuroblastoma after only 4 weeks. Given the established role of loss of CHD5 in development of neuroblastoma in humans, we are establishing the MYCN neuroblastoma model in our lab to characterize the ability of chd5 to act as a tumor suppressor in zebrafish in this context. Establishment of such a model would greatly facilitate subsequent determination of how loss of chd5 contributes to tumorigenesis.
The long-term goal of the Ogas lab is to understand how CHD5 suppresses tumor formation and development and to use this understanding to develop novel anti-tumor strategies. Establishment of an experimentally robust role for chd5 in tumor suppression and gene expression in zebrafish will enable us to use the diverse suite of experimental tools available in this model system to characterize the mechanism of action of CHD5 in vertebrates and to identify strategies to suppress growth of tumors associated with loss of CHD5. At the conclusion of the studies described above, we will have the tools necessary to undertake a chemical genetic screen for compounds that suppress chd5-dependent defects during embryogenesis. Such chemicals would represent terrific lead compounds for development of pharmaceuticals to treat CHD5-dependent tumors. In addition, our proposed research will enable us to use the formidable forward and reverse genetic tools available in zebrafish to identify additional epigenetic machinery that contributes to CHD5-mediated tumor suppression. Identification of such machinery will also facilitate development of new mechanistically-based therapeutic strategies.
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Current Collaborations Dr. Roger Deal Emory University, Atlanta, Georgia Genome-wide analyses of PICKLE in Arabidopsis Dr. Heng Zhang Shanghai Center for Plant Stress Biology, Shanghai, P. R. China Genome-wide analyses of PICKLE in Arabidopsis
Dr. Scott Briggs Purdue University, West Lafayette, Indiana Establishment of zebrafish model system for H3K27M gliomas Dr. Clint Chapple Purdue University, West Lafayette, Indiana Determination of the functional relationship between Mediator and H3K27me3 Dr. Eric Deemer Purdue University, West Lafayette, Indiana Evaluation of the effect of participation in SSP in persistence in STEM Dr. Brian Dilkes Purdue University, West Lafayette, Indiana Genetic analysis of PICKLE in Arabidopsis and chd5 in zebrafish Dr. Mark Hall Purdue University, West Lafayette, Indiana Identification of subunits of CHD5 chromatin remodeling complex Dr. Beth Tran Purdue University, West Lafayette, Indiana Analysis of role of DEAD box / RING finger proteins in seed development
8. Evidence of Interdisciplinary Activity
Purdue University Center for Cancer Research – Associate Director with responsibility for Cancer
Research Career Enhancement 2018 – PCCR review committee for Challenge and Phase II Competitions 2017 PULSe training group Chromatin and Regulation of Gene Expression (ChaRGE)
– Recruitment and Curriculum Committee member 2013 – 2014 – Executive Committee member 2003-6
Biochemistry and Molecular Biology – Temporary Advisory Committee member 1999 Purdue Genetics Program – Exam Committee member 1999 Plant Biology Program – Admissions Committee Chair 1999-2002 Plant Biology Program – Seminar Committee Chair 1999-2000
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9. Reviewer for Professional Journals
BBA, ad hoc Development, ad hoc G3, ad hoc Journal of Experimental Botany, ad hoc Journal of Integrative Plant Biology, ad hoc Molecular General Genetics, ad hoc Molecular Plant, ad hoc Nature, ad hoc Nature Communications, ad hoc New Phytologist, ad hoc Nucleic Acids Research, ad hoc Plant Cell, ad hoc Plant Journal, ad hoc Plant Molecular Biology, ad hoc Plant Physiology, ad hoc PLoS Genetics, ad hoc Proceedings of the National Academy of Sciences, ad hoc Science, ad hoc Trends in Genetics, ad hoc
10. Reviewer for Grants
Agriculture and Agri-Food Canada Department of Energy National Science Foundation Natural Sciences and Engineering Research Council of Canada United States Department of Agriculture Member of National Science Foundation Plant and Microbial Developmental Systems Advisory Panel,
October 21-22, 2004 Member of National Science Foundation Gene Regulation and Epigenetics Advisory Panel, October
13-15, 2010 Member of National Science Foundation Plant Fungal and Microbial Developmental Mechanisms and
Evolution of Development Mechanisms Advisory Panel, October 12-14, 2011. Member of National Science Foundation Proposal Review Panel, February 2015. American Heart Association Peer Review Committee, April 2016.
11. External Reviewer
National Science Foundation Committee of Visitors for the Division of Biological Infrastructure, June 16-18, 2004
12. Guest Editor
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Special issue of Biochimica et Biophysica Acta (BBA) - Gene Structure and Expression titled: Plant Chromatin: Structure and Expression (Volume 1769 Issues 5-6, published May-June 2007). 15 articles on topics related to plant chromatin were included in this issue. Guest Associate Editor for PLoS Genetics for 1 submission in 2013.
13. Editorial Board Member of Editorial Board for Biochimica et Biophysica Acta (BBA) - Gene Regulatory Mechanisms. 9/2009-present.
14. Session Chair at meeting co-Chair of “Chromatin and Genome Integrity” session of Chromatin and Epigenetics Symposium at Purdue University on October 11, 2016. Co-Chair of “Epigenetics: from development to aging” session of Mid-West Regional Society for Developmental Biology meeting at Case Western Reserve University in Cleveland, OH on Sept 14-16, 2018.
Part II: Section B “LEARNING” Teaching statement
My general philosophy with regards to teaching is that the instructor should try and make the subject matter as accessible as possible. Different students learn in different ways, and I do my best to accommodate as many different learning styles as possible. Given that different student populations will enroll in different classes, it is necessary to change delivery and expectations depending on the class. In general, however, I strive for a friendly engaging approach and do my best to place the material in a context that the students can readily relate to. One tool I particularly have embraced as of late is use of online assignments on Blackboard. I frequently assign homework that is relevant to the lecture of the day and make it due the night beforehand. I then read the assignments prior to class and use the responses of the students to help direct the lecture for that day. I am currently responsible for two distinct courses with two distinct goals. AGR 11500 is the departmental section of AGR 10100, which is a 1 credit course that all freshmen entering the College of Agriculture are required to take. My goal in this class is not to teach them biochemistry but rather to help them to successfully make the transition from high school student to Purdue undergraduate. Notice that I don’t say Purdue biochemist. We know that typically thirty to fifty percent of the freshmen class will elect to switch majors. I try to explain our program and expectations as best I can so that students can better (and more rapidly) decide if Biochemistry is the right program for them. I talk about our curriculum and how the courses fit together. I also talk about non-curricular issues such as internships and leadership activities that help students achieve greater success. I particularly emphasize the importance of undergraduate research in our program and how doing science is so much more than reading textbooks. Throughout the class, I have students read articles in the popular press (typically from the New York Times) that help to ground subsequent discussions in class.
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I also teach BCHM 46500, which students typically take the last semester of their senior year. At this point in the curriculum, our students have taken the equivalent of all of the biochemistry courses that we expect of our incoming graduate students. As a result, I use the course as an opportunity to teach them how to use the biochemistry they have been learning rather than to teach them more biochemistry. I emphasize critical thinking and careful application of the scientific method. The majority of the class is based on primary literature, which previous students have indicated is the portion of the class that they appreciated the most. We take about 6-8 lectures to go through a paper, and the students are responsible for understanding the entire paper in substantial detail. One of the goals of this endeavor is to help students to appreciate how much careful work is necessary to generate the figures they have been seeing in their textbooks. The students are required to do literature searches to get them used to finding information on their own (and assessing its robustness) and to help wean them from their reliance on textbooks as sources of information. Extensive class participation is encouraged to encourage peer-to-peer learning.
1. Courses taught Dr. Ogas strongly believes in the fundamental importance of teaching. This belief is demonstrated by the many opportunities he has taken to engage in teaching as an activity. From 2000 – 2004, Dr. Ogas’ primary teaching responsibilities were BCHM 562 and BCHM 691. BCHM 562 is a 3 credit upper level undergraduate course that Dr. Ogas taught in the fall. Dr. Ogas shared teaching responsibilities with Dr. Harry Charbonneau and was responsible for 20 lectures in the second half of the semester. The material that Dr. Ogas covered was primarily focused on subject matter related to the central dogma of molecular biology. Average enrollment: 41 Average course rating: 4.0 Average instructor rating: 4.3 BCHM 691 was a 2 credit graduate course taught in the spring. Dr. Ogas developed the material for the course, which was titled “Biochemistry of the cell cycle”. The primary focus of the course was to familiarize students with budding yeast as a model system and how it has been used to study regulation of the eukaryotic cell cycle. Average enrollment: 13 Average course rating: 4.2 Average instructor rating: 4.5 From 2005 – 2008, Dr. Ogas taught BCHM 601, which was a 2 credit course for first year graduate students in the Department of Biochemistry. This course emphasized analysis of scientific literature and was team taught by the faculty of the Department. Dr. Ogas was personally responsible for the first 8 hours of lecture as well as for organizing the presentation schedule for the remainder of the classes (in which he also participated). Average enrollment: 5 Average course rating: 4.7 Average instructor rating: 4.6
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Since 2005, Dr. Ogas has taught BCHM 465 (formerly BCHM 565). BCHM 465 is a 2 credit course for the Biochemistry undergraduate majors in their final year. Dr. Ogas uses this opportunity to emphasize critical thinking and application of biochemistry to real world problems. The students are asked to critically analyze the primary research literature. Class discussion is heavily emphasized, and students are frequented asked to work in small groups during class. Semester Enrollment Course rating Instructor rating 2005(S) 8 4.0 4.1 2006(S) 16 4.0 3.8 2008(S) 13 3.9 4.5 2009(S) 21 4.5 4.2 2010(S) 21 4.2 4.5 2011(S) 26 4.5 4.6 2012(S) 14 4.1 4.2 2013(S) 21 4.6 4.7 2014(S) 30 4.1 4.0 2015(S) 25 4.0 4.6 2016(S) 39 4.2 4.3 2017(S) 27 3.8 4.5 2018(S) 34 4.0 4.2
Since Fall of 2008, Dr. Ogas has taught the Departmental section of AGR 101 (now given a separate course number, AGR 115). AGR 101 is a 1 credit course that all freshmen entering the College of Agriculture are required to take. The Departmental section consists only of Biochemistry freshmen. Dr. Ogas has revised the course to focus on introduction to the diverse academic and research opportunities in the major, critical thinking, and the scientific process. Class discussion is heavily emphasized, and students are assigned readings and homework prior to each class that are then discussed in class. Semester Enrollment Course rating Instructor rating 2008(F) 26 4.1 4.9 2009(F) 30 4.3 4.8 2010(F) 31 4.1 4.6 2011(F) 26 4.1 4.4 2012(F) 22 4.4 4.9 2013(F) 13 4.1 4.8 2014(F) 29 4.3 4.6 2015(F) 30 4.1 4.8 2016(F) 47 4.2 4.8 2017(F) 34 4.6 4.8 2018(F) 50 4.6 4.8
BCHM 660 (Structure, Function of Nucleic Acids) is a 1 credit course for first year graduate students. This course is critical treatment of structure-function relationships of nucleic acids that serves as an introduction to the fundamental biochemical properties of nucleic acids for graduate students in many different
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programs. Dr. Ogas took responsibility for this course while the normal instructor, Dr. Barbara Golden, was on sabbatical. He presented 8 of the 14 lectures. Semester Enrollment Course rating Instructor rating 2007(F) 65 3.9 4.2
In addition to the aforementioned courses, Dr. Ogas has also taken several opportunities to contribute to other courses. He often fills in for other instructors as a guest lecturer for a relevant topic in their course. Finally, he engaged in a truly interdisciplinary activity when he was a guest lecturer in an English course (ENGL 373) in which he spoke about his views about the relationship between science fiction and science and the role that each plays in driving the other. Total courses: 12 Total guest lectures: 38 Total students: 1,020
Other teaching activities Dr. Ogas believes that one of the most important contributions that a faculty member can make to an undergraduate’s education is to give them experience doing actual laboratory research. He feels that this activity gives highly motivated undergraduates the opportunity to explore whether or not they are interested in pursuing a Ph. D. in science. Perhaps more importantly, he feels that the experience gives all of the students first-hand experience at how scientific knowledge is garnered and, he hopes, an appreciation of basic research as a worthwhile endeavor. In total, Dr. Ogas has had 94 undergraduates and 8 high school students work in his lab (including 64 women, 14 members of underrepresented groups, and 3 study abroad students). These undergraduates have contributed to a variety of undergraduate projects involving genetics, biochemistry, and/or molecular biology in Arabidopsis and/or zebrafish. In total, these 92 undergraduates have undertaken 130 semesters of research for credit, 40 summer semesters supported by NSF, HHMI, or similar programs, and 88 semesters of research for pay (largely as NSF participants). As noted above, the efforts of these students has resulted in 9 undergraduate authorships on 8 peer-reviewed papers. In addition, Dr. Ogas has hosted 5 high school students (3 male and 2 female) in the lab for projects that were then entered into science fairs.
Dr. Ogas has supervised the following undergraduate research projects:
Angela Russell (BCHM 498) 1999-2000. Angela helped carry out a genetic screen for gibberellin signal transduction mutants.
Michelle Fredette (BCHM 498) Summer 2001-Summer 2002. Michelle helped carry out a genetic screen for gibberellin signal transduction mutants and then helped to determine their map location.
Jennifer Robey (BIOL 494) Spring 2002. Jennifer aided in the phenotypic characterization of pkr2 plants.
Monica Alvarez (BCHM 498) Spring 2002-Summer 2002. Monica helped carry out a genetic screen for activation tagged mutants that exhibited increased fat accumulation.
Kristen Roseberry (BCHM 498) 2001-Summer 2002. Kristen helped carry out a genetic screen for activation tagged mutants that exhibited increased fat accumulation.
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Linda Quach (BIOL 494, BCHM 498) 2001-Summer 2003. Linda helped carry out a genetic screen for activation tagged mutants that exhibited increased fat accumulation.
Alexis Simons (BCHM 498) Fall 2002 – Spring 2004. Alexis helped further characterize the phenotype of a mutant that made trichome formation dependent on gibberellin in pkl plants.
Megan O'Shaughnessey (BCHM 498) Fall 2004 – Fall 2005. Megan examined the role of other chromatin remodeling factors in PKL-dependent repression.
Yoshiaki Hagiwara (BCHM 498) Fall 2004 – Fall 2005. Yoshi examined the role of other chromatin remodeling factors in PKL-dependent repression.
Holly Courtney (School of Agriculture) Spring 2005 – Fall 2005. Holly characterized the effect of a dominant negative allele of PKL on wild-type plants.
Courtney Chambers (School of Science) Spring 2005 – Spring 2006. Courtney examined the effect of gibberellin on PKL protein expression.
Megan West (BCHM 498) Spring 2006 – Fall 2006. Megan examined the role of RGL2 in the GA-dependent PKL-independent repression pathway. She also studied developmental regulation of GA responsiveness.
Dustin Owens (BCHM 498) Spring 2007 – Spring 2008. Dustin used a reverse genetics approach to examine the contribution of other chromatin remodeling factors to PKL-dependent silencing.
Pooja Patel (BCHM 498) Fall 2008 – Spring 2009. Pooja helped carry out a reverse genetic analysis of chromatin remodeling factors in Arabidopsis.
Camellia Reyes (BCHM 498) Spring 2009 – Fall 2009. Camellia helped carry out a reverse genetic analysis of chromatin remodeling factors in Arabidopsis.
Donghui Li (BCHM 498) Spring 2010 – Spring 2011. Donghui helped carry out a reverse genetic analysis of chromatin remodeling factors in Arabidopsis. She also carried out a chemical genetic screen. In 2011, Donghui was accepted into a PhD program at Johns Hopkins.
Whitney Ringenberg (NSF REU, BCHM 498) Summer 2010 – Spring 2011. Whitney helped carry out reverse genetic analysis of T-DNA alleles of PKR2 and assisted in genetic crosses between pkr2 and other mutant plants. She also helped to characterized transgenic pkl lines carrying domain deletion constructs of PKL. In 2011, Whitney accepted a position at Cargill.
Allie Shockley (BCHM 498/NSF REU 2011) Fall 2010 – Spring 2012. Allie undertook double mutant analysis of CHD genes in Arabidopsis (PKL, PKR1, and PKR3). In the summer of 2011 she was supported by an NSF REU and examined the role of PKL and PKR2 in endosperm development and imprinting. In 2012, Allie was accepted into the Indiana University School of Law.
Nyema Harmon (BCHM 298) Summer 2012. Nyema helped Monica and Erin with characterization of pkl and wt T2 seed.
Nyemade Harmon (BCHM 298) Summer 2012. Nyemade helped Monica and Erin with characterization of pkl and wt T2 seed.
Amanda Smith (BCHM 498) Fall 2011 – Fall 2012. Amanda examined the role of PKL and PKR2 in seed development. In 2013, Amanda Smith was accepted to IU School of Medicine.
Kim Tyler (BCHM 298/498, HHMI REU Summer Program 2012) Spring 2011 – Spring 2013. Kim worked with Whitney to do PCR and confirm presence of domain deletion constructs of PKL and also did westerns to confirm expression of altered protein while participating in BCHM 298. Her BCHM 498 project involved examining CHD5 gene expression in zebrafish organs. Her HHMI project involved in situ analysis of CHD5 in zebrafish and characterization of chd5 morphants. In 2013, Kim was accepted into a PhD program in the Department of Chemistry at the University of Wisconsin.
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Lotti Brose (HHMI REU Summer Program/BCHM 498) Summer 2011 – Spring 2013. Lotti helped to characterized transgenic pkl lines carrying domain deletion constructs of PKL. In 2013, Lotti was accepted into a PhD program at UC Santa Cruz.
David Loring (BCHM NSF REU) Summer 2013. David did western analysis of transgenic Arabidopsis lines carrying domain deletion alleles of PKL, carried out phenotypic analysis of same, and carried out M2 screen using PKL-GR line.
Erin Nicklow (NSF REU; BCHM 498) Summer 2012 – Fall 2013. Erin characterized pkl and wt T2 seed expressing deletion alleles of PKL and helped screen through pkl M2 and M3 seed. In 2014, Erin was accepted into the PhD program in BMCB at Cornell.
Jessie Wade (BCHM 498) Spring 2013 – Fall 2013. Jessie helped with the mutant screen using PKL-GR seeds. Jessie took a position in product development with Kimberly-Clark.
Kyle McCarthy (NSF REU/BCHM 498) Summer 2011 – Spring 2014. Kyle continued the chemical genetic screen initiated by Donghui, examined the effect of PKL and PKR2 on seed size, and helped with a mutant screen using PKL-GR seeds. In 2014, Kyle was accepted into a PhD program in plant breeding at MSU.
Monica Bomber (NSF REU/BCHM 498) Summer 2012, Spring 2013 – Spring 2014. Monica characterized pkl and wt T2 seed expressing deletion alleles of PKL and helped screen through pkl M2 and M3 seed. She also helped characterize the expression of CHD5 in zebrafish and the phenotype of zebrafish embryos with reduced expression of CHD5. In 2014, Monica was accepted into a PhD program at Vanderbilt.
Abha Gokhale (BIOL 294, Center for Cancer Research summer support) Spring 2013 – Fall 2015. Abha helped characterize transgenic pkl and wild-type carrying domain deletion constructs of PKL. In 2016, Abha was accepted into a biotech position in Chicago.
Quinton Nannet (BCHM 298 for 1st semester then BCHM 498) Fall 2013 – Spring 2015. Assisted in identification and phenotypic characterization of double mutants that lack PKL and other epigenetic regulators. Carried out screen for mutations that enhance flowering or seed filling phenotype of pkl plants. In 2016, Quinton was accepted into the Indiana University School of Medicine.
Rob Painter (HHMI REU Summer Program 2014, BCHM 498, NSF participant) Spring 2014 – Spring 2016. Rob helped carried out mutant screen of PKL-GR M3 seeds. In 2016, Rob was accepted into the Indiana University School of Medicine.
Lucas Banter (BCHM 498, HHMI REU Summer Program 2015) Fall 2014 – Spring 2016. Lucas helped carry out for mutant screen for enhancers of pkl-associated phenotypes. In 2017, Lucas was accepted into the Indiana University School of Medicine.
Jordyn Lucas (BCHM 498, NSF REU Summer 2015, NSF participant) Fall 2014 – Spring 2016. Jordyn helped to characterize the stress phenotypes of plants lacking various histone methyltranferases. In 2016, Jordyn was accepted into a PhD program in Biology at University of Missouri, Columbia.
Aysha Davis (LSAMP, LSAMP Summer 2015) Spring 2015 – Summer 2016. Aysha helped with identification of lines for INTACT, characterized the phenotypes of domain deletion alleles of PKL, and helped carry out for mutant screen for enhancers of pkl-associated phenotypes.
Kyle Ernzen (Biochemistry program NSF REU) Summer 2016. Kyle helped purify recombinant D domain from PKL for biochemical characterization.
Jenna Heiser (BCHM 298, NSF participant, BCHM 498) Spring 2015 – Spring 2017. Jenna helped with identification of lines for INTACT.
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Bret Small (NSF participant) Fall 2016 – Spring 2017. Bret helped carry out the mutant screen for enhancers of pkl-associated phenotypes.
Jasmin Gonzalez (NSF participant) Fall 2016 – Spring 2017. Jasmin helped carry out the mutant screen for enhancers of pkl-associated phenotypes.
Henry Richburg (Biochemistry program NSF REU) Summer 2017. Henry helped purify recombinant D domain from PKL for biochemical characterization.
Mark Gee (BCHM 498) Spring 2017 – Fall 2017. Mark carried out a screen for chemicals that phenocopy loss of PKL and generated amiRNA lines that reduced expression of SIRT1.
Mary Witucki (NSF participant, NSF REU Summer 2015, BCHM 498, cancer center summer 2016) Summer 2014 – Spring 2018. Mary helped identify double mutants in Arabidopsis using phenotypic analysis and PCR. In addition, she analyzed CRISP-cas generated lines of zebrafish using heteroduplex analysis. In 2018, Mary was accepted into a PhD program in biochemistry at Boise State.
Jackie Phipps (SURF Summer 2015, NSF REU Summer 2016, BCHM 498 NSF participant spring 2017) Summer 2015 – Spring 2018. Jackie helped with identification of lines for INTACT, carry out a mutant screen for enhancers of pkl-associated phenotypes, and generate amiRNA lines for PKL, DEAD-box proteins, and a sirtuin histone deacetylase. In summer of 2018, Jackie accepted a position with a biotech start-up in South San Francisco, CA.
John Petroskey (BCHM 298, NSF REU Summer 2016) Spring 2016 – Spring 2018. John helped identify T-DNA alleles of genes that possibly work with PKL to determine developmental identity. In addition, he helped carry out mutant screen for enhancers of pkl-associated phenotypes. In 2018, John was accepted into the Indiana University School of Medicine.
Katherine Poston (NSF participant) Fall 2016 – Fall 2018. Katherine helped identify T-DNA alleles of genes that possibly work with PKL to determine developmental identity.
Zachary Zelten (NSF participant) Fall 2016 – Spring 2018. Zachary identify T-DNA alleles of genes that possibly work with PKL to determine developmental identity.
Taylor Sabato (NSF participant, SURF participant) Fall 2016 – Spring 2018. Taylor helped genotype fish in a project to characterize a tumor suppressor in zebrafish.
Evan Baker (NSF participant) Spring 2018 – Fall 2018. Evan helped generate double mutants of interest in Arabidopsis.
Eleanor Logue (NSF participant) Spring 2018 – Fall 2018. Eleanor helped to characterize CRISPR-mutagenized zebrafish lines.
Elizabeth Walker Tindall (BCHM 298) Spring 2018 – Summer 2018. Walker helped to generate double mutants of interest in Arabidopsis.
Joey Dean (BCHM NSF REU) Summer 2018. Joey helped to generate and phenotypically characterize double mutants of interest in Arabidopsis.
Emily Overway (NSF participant, BCHM 498, volunteer) Summer 2016 – Fall 2018. Emily helped carry out the mutant screen for enhancers of pkl-associated phenotypes. In addition, she helped identify conditional pkl pie1 PKL-GR lines and biochemically purify domains of PKL protein.
Ellen Denning (NSF participant, PCCR recipient summer 2017) Fall 2016 – present. Ellen helped genotype fish in a project to characterize a tumor suppressor in zebrafish.
Chris Roberts (BCHM 298) Fall 2016 – Spring 2019. Chris helped genotype fish in a project to characterize a tumor suppressor in zebrafish. In addition, he helped carry out a mutant screen in Arabidopsis, and helped to generate double mutants.
Christian Arie Jenkins (BCHM 298) Spring 2018. Arie helped generate double mutants in Arabidopsis related to PKL-dependent pathways.
Emily Johnson (BCHM 298, Summer 2019 MASI) Spring 2018 – present. Emily helped generate double mutants in Arabidopsis related to PKL-dependent pathways.
Colin Hemme (BCHM 298, Summer 2019 MASI) Spring 2018 – present. Colin helped generate double mutants in Arabidopsis related to PKL-dependent pathways.
Lauren Courtney (BCHM 298) Spring 2018. Lauren helped generate double mutants in Arabidopsis related to PKL-dependent pathways.
Jaelen Nice (BCHM 498) Spring 2018. Jaelen helped generate double mutants in Arabidopsis related to PKL-dependent pathways.
Abby Anderson (BIOL 498) Fall 2019. Abby helped to genotype fish in a project to characterize a tumor suppressor in zebrafish.
Dr. Ogas has supervised the research of the following undergraduates while they worked in the lab as research assistants:
Tisha Eng (School of Agriculture, Biochemistry) Spring1999- Spring 2000. Tisha studied the relationship between gibberellin and root elongation.
Dan Henry (School of Science, Mechanical Engineering) Fall 1999- Spring 2000. Dan studied the genetic interaction between GAI and PKL, two factors involved in perception of GA.
Collin Mitchell (School of Agriculture, Biochemistry) Spring 2000 – Spring 2001. Collin studied the relationship between ethylene and gibberellin, two plant growth regulators.
Michelle Fredette (School of Science, Genetic Biology) Fall 2000 – Summer 2001. Michelle helped carry out a genetic screen for gibberellin signal transduction mutants and then helped to determine their map location.
Katie English (School of Agriculture, Biochemistry) Spring 2000 – Summer 2001. Katie helped carry out a genetic screen for gibberellin signal transduction mutants.
Jessica Posto (Indiana University) Summer 2001. Jessica helped carry out a genetic screen for activation tagged mutants that exhibited increased fat accumulation.
Kerry Behnke (School of Agriculture, Biochemistry) Fall 2000 – Spring 2002. Kerry helped carry out a genetic screen for gibberellin signal transduction mutants.
Ki-jeong Park (School of Agriculture, Biochemistry) Fall 2001 – Spring 2002. Ki-jeong helped carry out a genetic screen for activation tagged mutants that exhibited increased fat accumulation.
Darren Egbert (School of Agriculture, Agronomy) Summer 2001 – Fall 2002. Darren helped carry out a genetic screen for activation tagged mutants that exhibited increased fat accumulation.
Alexis Simons (School of Agriculture, Biochemistry) Fall 2001 – Spring 2002. Alexis helped carry out a genetic screen for activation tagged mutants that exhibited increased fat accumulation.
Laura Sheetz (Indiana University) Summer 2002, Summer 2003. Laura helped carry out a genetic screen for activation tagged mutants that exhibited increased fat accumulation.
Jonathon Hittle (School of Management) Spring 2003. Jonathon helped carry out a genetic screen for tagged mutants that exhibit increased pickle root penetrance.
David Ly (School of Management) Spring 2003. David helped carry out a genetic screen for tagged mutants that exhibit increased pickle root penetrance.
Ryan Dumas (Indiana University) Summer 2003. Ryan did genetics and PCR to identify a double mutant of Arabidopsis defective in chromatin remodeling.
Jacob Gerber (Washington University) Summer –Fall 2003. Jacob helped determine the expression pattern of a GFP reporter construct.
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Matt McDermott (School of Science) Fall 2003. Matt helped to map the location of a gene involved in fat accumulation.
Amber Young (School of Science) Fall 2003 – Spring 2004. Amber helped to determine the number of complementation groups from a genetic screen.
Jessica Jones (School of Science) Fall 2003 – Spring 2004. Jessica helped to determine the time of action of the PKL protein.
Kelly Jackson (School of Science, Biology) Summer 2002 – Summer 2004. Kelly helped carry out a genetic screen for activation tagged mutants that exhibited increased fat accumulation and helped carry out a genetic screen for tagged mutants that exhibit increased pickle root penetrance.
Holly Courtney (School of Agriculture) Fall 2003 – Fall 2004. Holly helped to map the location of a gene involved in fat accumulation.
Courtney Chambers (School of Science) Fall 2003 – Fall 2004. Courtney helped to map a gene that is involved in GA signal transduction.
Kim Han (School of Agriculture) Spring 2004. Kim helped to clone genes that promote embryo development.
Tyler McWilliams (School of Engineering) Fall 2002 – Summer 2005. Tyler helped carry out a genetic screen for activation tagged mutants that exhibited increased fat accumulation.
Lukasz Wylezinski (Vanderbilt University) Summer 2005, Summer 2006. Lukasz carried out a genetic screen for mutants with altered responsiveness to gibberellin.
Olivia Lares (School of Science) Spring 2003 – Spring 2006. Olivia helped carry out a genetic screen for tagged mutants that exhibit increased pickle root penetrance.
Bethany Kline (Indiana Wesleyan) Summer 2007. Bethany undertook reverse genetic analysis to identify genes involved in cell wall biosynthesis.
Sara McCullough (College of Agriculture, Biochemistry) Fall 2009 – Spring 2010. Sara undertook reverse genetic analysis to identify genes that contribute to determination of developmental identity. She also identified conditions suitable for a chemical genetic screen for compounds that phenocopy loss of PKL.
Lotti Brose (College of Agriculture, Biochemistry) Fall 2009 – Spring 2011. Lotti undertook reverse genetic analysis to identify genes that contribute to determination of developmental identity.
Amanda Smith (College of Agriculture, Biochemistry) Spring 2010 – Spring 2011. Amanda undertook reverse genetic analysis to identify genes that contribute to determination of developmental identity.
Monica Bomber (College of Agriculture, Biochemistry) Fall 2010-Spring 2012. Monica helped with a forward genetics screen to identify genes that contribute to epigenetic stability.
James Bowman (College of Agriculture, Biochemistry) Fall 2014 – Spring 2015. James helped with zebrafish husbandry.
Jenna Heiser (College of Agriculture, Biochemistry, NSF participant) Fall 2014, Spring 2016. Jenna helped with identification of lines for INTACT.
Jackie Phipps (College of Agriculture, Biochemistry, NSF participant) Fall 2014 – Spring 2015. Jackie helped with identification of lines for INTACT.
Dr. Ogas has supervised the research of the following high school students while they worked in the lab as research assistants:
Charlotte Hass, on her senior honors research project in Fall of 2001. Charlotte helped carry out a genetic screen for activation tagged mutants that exhibited increased fat accumulation.
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Matthew McConnell, summer research project in 2002. Matthew carried out a genetic screen for activators of fat accumulation in roots of pkl seedlings.
Lukasz Wylezinski, on his junior honors research project in Fall of 2002 – Summer 2004. Lukasz carried out a genetic screen for regulators of fat accumulation in roots of pkl seedlings. Lukasz senior project won a gold medal in the Senior Botany Category at the Lafayette Regional Science and Engineering Fair as well as a special award presented by the Purdue School of Agriculture given annually to any excellent project in each division that deals with agriculture.
Giuseppi Alkire, on his senior research project in the 2014-15 academic year. Giuseppi carried out a genetic screen for enhancers of pkl-dependent phenotypes.
Megan Beaver, on an independent project in the spring of 2015. Megan characterized T-DNA alleles of putative histone methyltransferases.
Emily Johnson, worked as NSF participant and generated double mutants of interest in Arabidopsis spring 2018.
Arden Shen volunteered as a rising high school senior in summer of 2018 and generated double mutants of interest in Arabidopsis.
Joshua Smith volunteered as a rising high school senior in spring of 2019 and generated double mutants of interest in Arabidopsis
Dr. Ogas has supervised the following students from the Department of Biochemistry Summer Internship Program:
Megan Sweeney, Summer 1999. Megan studied the relationship between gibberellin and root elongation.
Jennifer Victor, Summer 2000. Jennifer aided in the construction of a PKL::glucocorticoid receptor fusion protein.
Dr. Ogas recognizes the importance of engaging in science as a collaborative international endeavor. In an effort to provide his students with exposure to this aspect of scientific research, he has welcomed the opportunity to have undergraduates from other countries work in his lab.
Dr. Ogas supervised Anja Kuschinsky, a student from Technical University of Berlin, Germany for her “Studienarbeit”, a three month internship in the laboratory during Summer of 2000. Anja helped to characterize the pattern of gene expression in developing pickle roots.
Dr. Ogas supervised Magali Kocher, a student from the University of Neuchâtel, Switzerland for a 2 month IASTE internship during the Summer of 2003. Magali helped to identify targets of PKL through qRT-PCR verification of microarray data.
Dr. Ogas supervised Valerie Bühren, a student from the University of Dusseldorf for 30 hours/week during the 2019 Fall semester. Valerie helped generate and analyze combinatorial mutants in Arabidopsis lacking PKL and sirtuin proteins.
Dr. Ogas also recognizes the importance of having many voices contribute to scientific discovery. As a result, he has strongly embraced having people from diverse backgrounds work in his lab. Six of the undergraduates mentioned above (Monica Alvarez, Nyema Harmon, Nyemade Harmon, Olivia Lares, Camellia Reyes, and Aysha Davis) are members of minorities that are historically underrepresented in science. In addition, Dr. Ogas has supervised the following students from the MARC/AIM program, SROP, or the Department of Biochemistry REU program:
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Quang Nhat Tran, summer of 1999. Quang studied the role of ABA in expression of embryonic identity in pkl seedlings.
Arlene Garcia, summer of 2002. The title of Arlene’s research project was “Use of an activation-tagging strategy to identify genes capable of increasing oil production”.
Melissa Torres, summer of 2002. The title of Melissa’s research project was “Genetic screen of pkl enhancers from a T-DNA knockout population”.
Ninoshka Caballero, summer of 2013 (MARC-supported student from UPR Humacao). Ninoshka did western analysis of transgenic Arabidopsis lines carrying domain deletion alleles of PKL, carried out phenotypic analysis of same, and carried out M2 screen using PKL-GR line.
Marcus Jackson, summer of 2014 (BCHM REU). Marcus helped carry out a genetic screen for mutations that enhance pkl-dependent phenotypes.
Aysha Davis, spring 2015 – fall 2016 (LSAMP). Aysha helped generate INTACT lines for examining role of PKL in specific cell types.
Daniela Martir-Vargas, summer of 2015 (SROP) and 2016 (NSF REU). Daniela helped generate INTACT lines for examining the role of PKL in specific cell types. In 2017, Daniela was accepted into a Masters of Science program in Medical Sciences in Ponce Health Sciences University.
Carlos Guzman, summer of 2018 (SROP). Carlos characterized the novel phenotypes of double mutant plants.
Dr. Ogas also supervised the following students from the Louis Stokes Alliance for Minority Participation (LSAMP) summer research program:
Camellia Reyes, summer of 2009 and Fall of 2009. Camellia carried out a phenotypic analysis of Arabidopsis plants that lack the CHD remodeling factors PKR1 and PKR3.
Recognition of undergraduate research in the Ogas lab:
Allie Shockley – recipient of ARP research scholarship (2011-12). Kim Tyler – recipient of ARP research scholarship (2012-13). Monica Bomber – recipient of ARP research scholarship (2013-14). Erin Nicklow – recipient of the Honors College Award for the Life Sciences category at the 2013
Undergraduate Research Poster Symposium; recipient of recipient of ARP research scholarship (2013-14).
Ninoshka Caballero –selected to present orally at the 2013 Annual Biomedical Research Conference for Minority Students (ABRCMS) in November 2013.
Daniela Martir-Vargas – third place in Purdue SROP poster competition 2016. Taylor Sabato – "Top Research Poster" award at SURF poster competition 2017. 10 of these were
awarded from a pool of 102 posters.
Service Related to Teaching (Student Awards, Mentorship, Academic Program Development and Grants): Development and Implementation of an Internationally Recognized Summer Science Program in Biochemistry Dr. Ogas serves as the Director of Program Development for the internationally recognized and prestigious Summer Science Program (SSP). Since 2012, he has worked with the SSP to expand the program into the field of Biochemistry. In doing so, he initiated and spearheaded a long-term initiative to increase the exposure and further strengthen the academic caliber of the Biochemistry student body. SSP is an
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internationally recognized summer education program for rising high school seniors. Prior to the contributions of Dr. Ogas, it ran two programs based in astrophysics at the campuses of New Mexico Tech (Socorro, NM) and University of Colorado (Boulder, CO). SSP attracts hundreds of talented, motivated applicants from across the US and around the world. As one measure of the quality of the students that participate in the program, over 70% of SSP alumni in the past five years have become undergrads at MIT, Caltech, Stanford, or the Ivy League. Due in part to the contributions of Dr. Ogas, SSP received $300,000 in funding in 2013 from the Gordon and Betty Moore Foundation to develop a new curriculum for SSP. In the 2-year course of a highly competitive national search, Dr. Ogas contributed significantly to the eventual selection of a new program in Biochemistry developed by Dr. Hall and Dr. Paula here at Purdue that resulted in $112,149 in funding from SSP. Importantly, this initiative resulted in external funding for Dr. Mark Hall and Dr. Stefan Paula for two years ($64,960 in 2014-15 and $47,189 in 2016). The SSP Biochemistry program is now fully implemented https://summerscience.org/fungal-inhibitor-design/ and is a runaway success. In 2018, there were over 450 applicants for 36 positions in the program. Further, U.C. San Diego is now working with SSP to replicate the Biochemistry program at their campus. A UCSD faculty member and member of the National Academy of Sciences, Professor Susan Taylor, has recently joined the SSP Board of Trustees in part to facilitate this process. From the standpoint of the Department of Biochemistry here at Purdue, the desired goal of this effort is to bring 36 of the best and brightest rising high school seniors to our campus for a transformative experience that they will strongly associate with our program and that will subsequently influence their selection of an undergraduate institution. In addition, this endeavor showcases the commitment of the Biochemistry faculty to our education mission. To make this vision sustainable, Dr. Ogas has successfully secured external funding for the SSP/Purdue Biochemistry program from the Indiana Space Grant Consortium: $15,000 in 2017 and $25,000 in 2018. He has also secured funding from the provost for summer salary support of Drs Hall and Paula for 5 years to support their teaching efforts. In addition, Dr. Ogas is attempting to leverage the success of the SSP program by creating a new program designed to increase the number of underrepresented students in STEM that is based on SSP. He is the author and PI of a $2,500,000 5-year R25 proposal to the NIH addressing this critical need that was submitted this spring. Based on the success of the SSP/Purdue Biochemistry program, SSP has received a pledge of $250,000 from a donor to support development of a new SSP curriculum in metagenomics. Dr. Ogas is currently leading the effort to bring this curriculum to Purdue, where he will oversee development of this new program by Dr. Pete Pascuzzi (Purdue University Libraries, Health and Life Sciences, courtesy appointment in Department of Biochemistry). Development and implementation of additional programs in the Department of Biochemistry and the Purdue University Center for Cancer Research Dr. Ogas engages in numerous other activities to both grow and improve the undergraduate program in the Department of Biochemistry. Representative examples include creating an international research exchange program with University of Dusseldorf, designing and implementing a graduate certificate program (to promote research success by our students, in particular by first generation students), serving on the University Goldwater selection committee to be better able to advise students on how to craft successful applications, conversations with University Admissions and advisors from other programs to increase student recruitment, and also building relationships with companies like Dow AgroSciences (four funded
proposals for $10,500 to support our undergraduate program). Through these and other actions, Dr. Ogas continuously strives to improve the experience of our Biochemistry undergraduates and thereby engender continuing increases in both the caliber and the size of our departmental program. Based on his many contributions to the Department of Biochemistry and the Summer Science Program, Dr. Ogas was recently asked to serve as an Associate Director of the Purdue University Center for Cancer Research (PUCCR) and oversee efforts by the PUCCR to promote training and professional development for student (both undergraduate and graduate) and postdoctoral scientists. The $2,500,000 5-year R25 proposal that was mentioned above is the centerpiece of a new effort spearheaded by Dr. Ogas to increase participation of underrepresented students in cancer-related research, and builds on the themes of the importance of authentic research and community of practice. He is examining and revising (where necessary) current PUCCR-sponsored activities related to training and professional development, including rewriting fellowship application guidance and directions and promoting student interactions with visiting faculty. The Center is currently preparing for its 5-year renewal, and Dr. Ogas is playing a critical role in preparing for the site visit and developing the PUCCR plans for the next 5 years. Current new initiatives under active consideration include sponsoring a club for undergraduates interested in cancer research, facilitating development of a cancer minor, and helping to create a life sciences job fair to promote job opportunities for graduate students and postdoctoral scientists engaged in cancer-related research as well as other life scientists. Promoting community of practice in the Department of Biochemistry Dr. Ogas has served as option representative for the Department of Biochemistry since 2007. In 2018, he became the Associate Head of the Department of Biochemistry, and his primary responsibility is undergraduate education. Since 2007, the size of the undergraduate program has grown from 88 students to 184 students, and our students have won multiple prestigious awards. This growth in numbers and in the caliber of our students are the fortunate outcomes of intentional design. In Biochemistry, we engage our students in a “community of practice”. We emphasize the “practice of science” – in all its different guises – in addition to providing the curricular material necessary to engage in that practice in a meaningful fashion. Further, we include guidance on the social aspects of the scientific enterprise so that students can both more easily transition into our community and become actively engaged members in that community. Much of what Dr. Ogas does involves sharing our story and our values with our students in a variety of different contexts. Dr. Ogas meets with a number of potential undergrads either in person during recruiting events or on the phone when he has a conversation with accepted students about how Biochemistry would be a good fit with them. He meets with all incoming freshmen during STAR to help them decide on their courses for the first semester and begin their transition into our program. Dr. Ogas also meets once a semester with all incoming transfer or CODO students to similarly help them transition successfully into our program. In addition, he meets with the officers of the Biochemistry club formally once a year and informally at various times to see how the activities of that club are integrating with the overall experience of students in our program. Another important conversation Dr. Ogas is frequently called on to have is when he meets with a student who is not thriving in our community (typically due to academic reasons). These meetings involve providing guidance on how to be more successful in our program or helping them make a transition to another program that is a better path to success for that individual. Both of the courses Dr. Ogas teaches, AGR 115 and BCHM 465, are used in part to both build and improve our undergraduates’ participation in our community. AGR 115 is used as a critical opportunity to introduce
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our program – both with regards to expectations and with regards to “who we are” – to the freshmen and to emphasize the importance of working together to promote success. BCHM 465 is used in turn to ask our seniors how we have done as a program and how we might do even better in providing our students with both an education and a community. Dr. Ogas takes this feedback to the undergraduate curriculum committee (of which he is a member), and the committee considers whether we need to make any adjustments to the curriculum in response. Promotion of Student Learning, Success, and Awards A critical aspect of what Dr. Ogas does is promote recognition of the success of our students. This recognition is deserved by the students whom are nominated. Further, it is a powerful vehicle by which we recruit new students to our program as well as inspire similar actions by our current students. The numbers speak for themselves with regards to the success of this endeavor. In the 10 years prior to Dr. Ogas becoming the option representative, students from Biochemistry were awarded Outstanding Student in Agriculture a total of three times. Over the past 11 years since he started leading our undergraduate program, students from Biochemistry have been awarded Outstanding Student (Freshman, Sophomore, Junior or Senior) in Agriculture 19 times out of a possible 40, with a total of 9 academic programs in the College of Agriculture. Further, the Department of Biochemistry has had two G.A. Ross Award winners (outstanding senior male at Purdue: 2013 and 2016) and one Flora Roberts Award (outstanding senior female at Purdue: 2011). Dr. Ogas wrote a nomination letter for all three of the Ross and Roberts award winners as well as a letter for all of the COA winners through 2013. He continues to write letters for COA nominees (and more recently a successful nomination for the December 2013 Commencement Student Responder), but often now plays a role as editor for COA nomination letters. The success of Biochemistry students extends beyond these awards and are not dependent on nomination letters from Dr. Ogas. A highlight list of extremely meritorious awards includes 3rd-team USA Today All-USA College Academic Team (2010), two Goldwater scholarships (a national competition: 2011-12 and 2014), Astronaut Scholarship (2013), Gates Cambridge Fellowship (a national competition: 2015), two Cordova Leadership Awards (2015 and 2016), three memberships in the ASBMB Honor Society (2015 and 2016), and ten Mortar Board awardees. Importantly, the recognition of the achievements of our students also continues beyond their time here at Purdue. Four of our students have received NSF Graduate Research Fellowships since 2013. These are very competitive fellowships that are a testimony to the strength of the undergraduate program that has been created in the Department.
International teaching:
Dr. Ogas created and oversees a study abroad program for STEM students. This program was initiated in 2017 and is a partnership with the University of Dusseldorf. In this exchange program, Purdue students spend the summer at the University of Dusseldorf doing authentic research in an academic lab, and students from Dusseldorf take classes and do research in labs here at Purdue during the academic year. Dr. Ogas traveled to Dusseldorf in 2016 to help establish this novel experiential program. Dr. Ogas worked with Dr. Sam Yingst in the summer of 2006 to design a course that addressed the fundamentals of PCR and molecular biology at the veterinary science school of Kabul University in Afghanistan. There were 2 primary goals of this course:
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1. To provide veterinary graduates with basic background on PCR applications so that they can take appropriate samples, handle them properly to maximize their chances of being diagnostic, and interpret laboratory results received from the central veterinary laboratory 2. To provide a basic understanding of PCR theory to lab diagnosticians and veterinary faculty.
The students that participated in the course included 5th year veterinary students (about to graduate), veterinary faculty, and staff of the veterinary diagnostic laboratory in which PCR diagnostics are performed. Dr. Ogas helped to design the syllabus of the course and provided materials and assistance for the creation of the basic science lectures (approximately 10 hours of lecture time in total).
Grants related to teaching and training: Current Grants Source and role: Office of the Provost (PI) Title: Summer Science Program Memorandum of Understanding Total project period and amount of award: 06/01/17 – 8/31/21, 6.5 weeks summer salary for 2 Purdue faculty
for each summer to teach the SSP/Purdue Biochemistry program Pending Grants Source and role: National Institutes of Health (PI) Title: Coupling community of practice and authentic research to enhance diversity in cancer-related careers Total project period and amount of award: 4/01/2020 - 3/31/2025, $2,583,588 Past Grants Source and role: Indiana Space Grant Consortium (PI) Title: The 2018 Summer Science Program in Biochemistry at Purdue University Total project period and amount of award: 01/01/18 – 12/31/18, $25,000 Source and role: Indiana Space Grant Consortium (PI) Title: The 2017 Summer Science Program in Biochemistry at Purdue University Total project period and amount of award: 01/01/17 – 12/31/17, $15,000 Source and role: Summer Science Program (Program Director) Title: SSP/Purdue Biochemistry Pilot Program Total project period and amount of award: 06/01/16 – 8/31/16, $47,189 Source and role: Summer Science Program (Program Director) Title: Development of new curriculum in Biochemistry for SSP Total project period and amount of award: 09/01/14 – 8/31/15, $64,960 Source and role: Gordon and Betty Moore Foundation (consultant)
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Title: Planning Grant for Summer Science Program Expansion Total project period and amount of award: 10/01/13 – 9/30/16, $330,000 Role: These funds were used to screen for, select, and develop a new curriculum for SSP. Dr. Ogas helped develop the plan and the proposal and he played a leading role in implementing the stated goals. It was this and other efforts that resulted in successful development of the SSP/Purdue Biochemistry program. Source and role: Dow AgroSciences (PI) Title: The 2015 Dow AgroSciences Aid-To-Education Program Funds Total project period and amount of award: 01/01/11 – 12/31/11, $2,000 Source and role: Dow AgroSciences (PI) Title: The 2013 Dow AgroSciences Aid-To-Education Program Funds Total project period and amount of award: 01/01/13 – 12/31/13, $3,000 Source and role: Dow AgroSciences (PI) Title: The 2012 Dow AgroSciences Aid-To-Education Program Funds Total project period and amount of award: 01/01/12 – 12/31/12, $3,000 Source and role: Dow AgroSciences (PI) Title: The 2011 Dow AgroSciences Aid-To-Education Program Funds Total project period and amount of award: 01/01/11 – 12/31/11, $2,500 Activities related to teaching:
Member of HHMI sponsored Faculty Learning Community (FLC) in 2012. The overall goal of the four-year HHMI grant that supports this FLC is to infuse the concepts of statistics and experimental design into the undergraduate life sciences curriculum.
Recognition of contribution to undergraduate research:
Asked to serve on a panel that discussed undergraduate research after the Undergraduate Research and Poster Symposium in April 2005.
Recognition of teaching:
2003-4 Department of Biochemistry nominee for Outstanding Undergraduate Teaching Award. 2004-5 Department of Biochemistry nominee for Outstanding Undergraduate Teaching Award. 2017-8 Department of Biochemistry nominee for Outstanding Undergraduate Teaching Award.
Recognition of service to students: Biochemistry nominee for the College of Agriculture “2002-2003 Outstanding Service to Students Award”. Biochemistry nominee for the College of Agriculture “2007-2008 Outstanding Counselor Award”. Biochemistry nominee for the College of Agriculture “2008-2009 Outstanding Counselor Award”. Biochemistry nominee for the College of Agriculture “2009-2010 Outstanding Counselor Award”. Biochemistry nominee for the College of Agriculture “2010-2011 Outstanding Counselor Award”. Biochemistry nominee for the College of Agriculture “2011-2012 Outstanding Counselor Award”. Biochemistry nominee for the College of Agriculture “2012-2013 Outstanding Counselor Award”.
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Biochemistry nominee for the College of Agriculture “2013-2014 Outstanding Counselor Award”. Biochemistry nominee for the College of Agriculture “2014-2015 Outstanding Counselor Award”. Recipient of the College of Agriculture “2016-2017 Outstanding Counselor Award”.
Part II: Section C “ENGAGEMENT” 3. Organized Educational Activities
Presenter at Annual Biomedical Research Conference for Minority Students (ABRCMS) in
Indianapolis, Indiana on November 16, 2018. One of three presenters for one-hour presentation titled “The First Year of Graduate School: How to Survive and Thrive”.
SSP Director of Program Development 2018 – present. The Summer Science Program (SSP) is an internationally recognized residential science education program for exceptional high school students. In this role, Dr. Ogas is responsible for successful implementation of SSP Biochemistry program here at Purdue, developing new curricula for SSP, and promoting expansion of SSP at other universities.
Invited speaker for presentation for “Family Day” for high school students participating in Summer Science Program in Biochemistry at Purdue University July 7, 2018. “Using model organisms and genome editing to study cancer”.
Invited speaker for presentation to high school students participating in Summer Science Program in Biochemistry at Purdue University July 14, 2017. “Model systems and the epigenetics of cancer”.
Member of Expansion Planning Committee for the Summer Science Program (2014 – 2017). This committee coordinates all efforts (funding, curricular development, identification of new campus) to increase the size and curricular offerings of SSP.
Chair of the New Curriculum Committee for the Summer Science Program (2013 – 2017). This committee is responsible for identifying and helping to develop a new curriculum for SSP. This initiative is funded by a grant from the Gordon and Betty Moore Foundation in the amount of $300,000.
Panel member for discussion of undergraduate research at Honors College October 21, 2015. Invited speaker for presentation to LSAMP students regarding graduate school application process
December 4, 2014. Member of the Outreach Committee (2009 – 2012) that recruits underrepresented minorities for SSP. Helped teach four one-hour lectures on critical thinking to 4th-8th graders at New Community School
November 2009. Participated in round table discussion as member of Career Development Panel for Purdue Latino
Scholars Forum October 1, 2008. Judged poster competition at Purdue Latino Scholars Forum September 19, 2007. Presented poster at National Collegiate Inventors & Innovators Alliance, Portland, Oregon March 24,
2006. Presentation on earth science at New Community School May 2005. Lecture on genomics at WALLA, March 2001. Two presentations on genomics at P-CARET meetings Fall 2000.
6. Advising, Counseling, and Recruiting Students
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In addition to being the departmental option representative, I have also been the academic advisor for 70 undergraduates in the Department of Biochemistry. Serving in this capacity entails meeting with each student a minimum of once a semester typically for about 30 minutes to assist the student in achieving curricular and professional objectives.
Holly Courtney (2005-6, B.S. 2006) Emily Ferguston (2005-2006) Damon Jones (B.S. 2006) John Kronberg (B.S. 2006) Jessica Maraldo (2005-6) Stephanie Cutshaw (2005-2007) Michael Hanlon (B.S. 2007) Laurin McNight (2006-7) Duke LaMere (2005-7) Dustin Owens (B.S. 2008) Sharon Bainbridge (2009) Jillian Borsa (2007-2009) Kelvin Gann (2009) Lukas Ly (2009) Johannes Rungger (2009) Mary “Janie” Stine (2007-2009) Emily Sturm (B.S. 2009) Xue Cao (2010) Erin Kischuk(B.S. 2010) Nadia Atallah (B.S. 2011) Alejandra Boeker (B.S. 2011) Adam Dillard (B.S. 2011) Anna Hurlock (B.S. 2011) Jon Roose (2010-2011) Molly Scherer (2010-2011) Rachel Schluttenhofer (B.S. 2011) Leslie Seals (B.S. 2011) Jackie Huynh (2009-2012) Allison Shockley (B.S. 2012) Allison Ustynoski (2010-2012)
Elizabeth Baker (B.S. 2013) Christina Millhouse (B.S. 2013) Gabe Rangel (B.S. 2013) Mikala Hillis (2013-2014) Kyle McCarthy (B.S. 2014) Amanda Shanley (B.S. 2014) Jessica Wade (B.S. 2014) Jessica Gabbard (2011-2015) Samuel Schaffter (B.S. 2015) Evan Adams (2014-2016) Elizabeth Amundson (2014-present) Puja Banerjee (B.S. 2016) Michael Busche (B.S. 2016) Allyson Carpenter (2015-present) Arizona Fox (B.S. 2016) Mark Gee (2014-present) Jenna Heiser (2014-present) Kristen Hendricks (2014-present) Emma Lendy (B.S. 2016) Christopher Long (2014-2016) Ramya Modi (2014-present) Logan Richards (2014-present) Yi Wen (B.S. 2016) Michelle Weyreter (2007-2009) Kaitlyn Wolack (B.S. 2014) Lanchen Wu (B.S. 2016) Cole Wunderlich (B. S. 2016) Yu Xue (B.S. 2016) Larry Zhang (B.S. 2012) Elizabeth Ziga (B.S. 2016)
Summer Transition, Advising, and Registration (STAR) (formerly Day on Campus):
Meets with incoming freshmen and transfer students during the College of Agriculture’s session of STAR. Advise on Fall registration; direct to appropriate placement tests; instruct about any additional pre-registration issues as they arise. June 13-23, 2006 22 students June 12-22, 2007 27 students June 10-20, 2008 28 students June 16-29, 2009 30 students June 21-July 1, 2010 51 students June 20-June 30, 2011 36 students
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June 18-June 28, 2012 19 students June 17-June 27, 2013 21 students June 25-July 9, 2014 23 students June 15-25, 2015 22 students June 13-July 1, 2016 47 students June 19-July 7, 2017 32 students June 18-July 20, 2018 47 students June 14-July 12, 2019 44 students
Fall Preview Days: Met with high school seniors that were considering coming to Purdue (Fall, 2006). Talked about life as an undergraduate in the Department of Biochemistry and options that were available after graduation.
Graduate Recruiting:
Division of Natural Sciences and Mathematics, Wesleyan University, Indiana, April 2006. Invited to give 2 presentations to undergraduates in a Cell Biology class and in a Biochemistry class. The title of the presentation for the Cell Biology class was “Determination of when a chromatin factor regulates developmental identity”. The title of the presentation for the Biochemistry class was “Use of microarray analysis to identify targets of a chromatin remodeling factor” Division of Natural Sciences and Mathematics, Wesleyan University, Indiana, April 2005. Invited to give 2 presentations to undergraduates in a Cell Biology class and in a Biochemistry class. The title of the presentation for the Cell Biology class was “Determination of when a chromatin factor regulates developmental identity”. The title of the presentation for the Biochemistry class was “Use of microarray analysis to identify targets of a chromatin remodeling factor”.
7. Mentoring Faculty
Served on mentoring committees for the following Assistant Professors: Ann Kirchmaier (2005 – 7) Mark Hall (2007 – 2012) Jim Clemens (2006 – 2012) Xiaoqi Liu (2008 – 2012) Beth Tran (2009 – 2015) Sujith Puthiyaveetil (2017 – present) Leonor Boavida, Botany and Plant Pathology (2017 – present) Jeremy Lohman (2017 – present)
Served on mentoring committees for the following Associate Professors: Damon Lisch, Botany and Plant Pathology (2016 – present)
Presentation to assistant professors in Cell Identity and Signaling at Center for Cancer Research on October 10, 2016 at retreat regarding extramural funding: Launching a new cancer-related project in Danio rerio based on research in Arabidopsis thaliana.
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7. University or Departmental Administrative Committees Associate Head for Department of Biochemistry 2018 – Associate Director of Purdue University Center for Cancer Research with responsibility for Cancer Research Career Enhancement 2018 – STEM Advisory Board for the Goldwater Scholarship nominees for Purdue University 2014 – Department of Biochemistry Undergraduate curriculum, awards and activities committee 2009 – College of Agriculture Undergraduate Recruitment and Retention Committee 2007 – Department of Biochemistry Option Representative 2007 – 2018 University committee on formation of Office of Undergraduate Research 2016 Search committee for Department of Biochemistry faculty in plant biology 2015 –2017 Search Committee for Department Head of Biochemistry 2014 – 2015 College of Agriculture FEELS program advisory board member 2012 – 14 College of Agriculture Search Committee for Director for Center for Molecular Agriculture 2014 Department of Botany Faculty Search Committee external member 2013 – 4 Department of Biochemistry Advisory Group member 2004 – 7, 2008 – 2013 College of Agriculture ARP Food and Agriculture Assistantship Review Panel 2012 – 13 Department of Horticulture Faculty Search Committee external member 2011 – 12 Department of Biochemistry Undergraduate Curriculum Revision Committee 2008 – 9 Department of Biochemistry Honors Coordinator 2007 – 9 College of Agriculture Honors Committee 2007 – 9 Search Committee for Department Head of Biochemistry 2007 Department of Biochemistry Graduate Affairs/Recruiting (Chair) 2004 – 2007 PULSe training group Chromatin and Regulation of Gene Expression (ChaRGE) – Executive Committee member 2003 – 2006 WSLR building committee 2000 – , Chair effective 2004 Search committee for Biochemistry faculty member 2000 – 2002, 2004 Steering committee for Genomics Database Facility 2001 – 2004 Faculty advisor for the Biochemistry club 2000 – 2004 Biochemistry Graduate Advisory Committee 1999 – 2003 Biochemistry Leadership Review Committee 2003 Administrative/Professional Advancement Committee 1999 – 2003 PBP admissions committee chair 1999 – 2002 Search committee for Department Head 2000 – 2001 Search committee for Associate Dean of Agriculture/Director of Academic Programs 2000 – 2001 Departmental PRF review committee 2000 Minority graduate student recruitment and retention committee 1999 – 2001 ARP review committee 2000 PBP seminar committee chair 1999 – 2000 Grievance committee 1999 – 2001 PGP exam committee 1999 BMB Temporary Advisory committee 1999
